[Taxacom] Methodological plurality [was cladistic analysis for morphological characters -- UPGMA is not cladistics]

Dan Lahr dlahr at ib.usp.br
Mon Nov 19 07:29:34 CST 2012

Kip, I will have to steal this for thesis defenses:

"agreement of 5-7 different methods. Good feeling is the same as statistical
support, right?"


On Sat, Nov 17, 2012 at 3:27 PM, Kipling (Kip) Will <kipwill at berkeley.edu>wrote:

> On 11/15/2012 7:51 AM, Ashley Nicholas wrote:
> > I guess they do this to assess if there is any congruence in the results
> of all three analytical methods?
> On 11/17/2012 6:42 AM, Dan Lahr wrote:
> > More interestingly though, you raise an issue that has always bothered
> me:
> >people using multiple reconstructions methods.  I'll start by saying I do
> >not have a strong stance nor the answers to this question.
> >
> > In principle, it seems philosophically incoherent
> This is a point that triggers my peeve response. The incoherence Dan
> refers to being the root of my discomfort. Different methods have
> unique, but partially overlapping, ontological and epistemological
> starting points and so their congruence cannot be considered to mean
> much of anything at all. And yet, many (most?) publications throw the
> "big three" (ML, Pars, Bayes) at every data set, almost never explaining
> why or what it means, usually then one is picked (with little
> explanation why that one) and the rest ignored. I have facetiously
> suggested to people that if they add UPGMA and NJ that they might feel
> even more warm and fuzzy (or Poy, traditional Hennigian, SWAG, etc.),
> given agreement of 5-7 different methods. Good feeling is the same as
> statistical support, right?
> Congruence or conflict across methods tells us little or nothing about
> clade support.
> 1. These are not independent data being run using the different methods
> so this fails to be support through consilience. If two people that view
> the same world (the data) differently, come to the same result they
> could just as well both be wrong or both be right. That agreement (or
> lack) tells us little about the result, perhaps more about the methods.
> Using Pars for morphology and, for example, ML for DNA sequence data,
> may be a situation where one can invoke consilience, but I doubt that is
> to be preferred over a combined analysis.
> 2. If one cast all methods to be a form of one particular method (e.g.
> parsimony is just one model of likelihood) and thinks of using the
> different methods as a "sensitivity" analysis, then it is a very poor
> sensitivity analysis indeed. We have many much better ways to explore
> sensitivity of results across parameter space.
> 3. If congruence is thought of as a measure of support, even as a vague,
> number-free tingly feeling, and if we want to maximize that congruence,
> then this is maximized where all methods converge, which would probably
> can be achieved by using model parameters in ML, etc, to fit parsimony.
> Of course that would be a silly thing to do, unless you really believe
> congruence across methods means something. I don't see statisticians
> using multiple different tests and then implying or claiming that since
> those three test all (or say 2 out of 3) had significant p=values the
> result is "more significant" (increased "truthiness"?).
> It is legitimate to do a comparison of methods for its own sake, they
> each have properties worth exploring, but that is rarely what is
> published. One may wish to specifically test certain assumptions, again
> that is valid, but when there is no explanation for the methodological
> plurality, or a simple statement that implies support, e.g. "ML and Pars
> gave basically the save topology" and nothing more, it seems a waste of
> time. If its phylogeny, topology or evolution along branches one is
> after, then pick the appropriate method, justify it and understand its
> limitations.
> Echoing this-
> On 11/17/2012 6:42 AM, Dan Lahr wrote:
> > you should choose a strategy and stick with it, many of the different
> analytical methods are logically incompatible.
> yep, Dan is right.
> kip
> --
> Contact info:
> Kipling W. Will
> Associate Professor/Insect Systematist
> Associate Director,Essig Museum of Entomology
> send specimens to:
> Essig Museum of Entomology
> 1101 Valley Life Sciences Building, #4780
> University of California, Berkeley
> Berkeley, CA 94720-4780
> letter mail to:
> 130 Mulford Hall
> ESPM Dept.- Organisms & Environment Div.
> University of California
> Berkeley, California 94720
> fax 510-643-5438
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Daniel J. G. Lahr, PhD
Dept of Zoology, Univ. of Sao Paulo, Brazil

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